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1.
Perturbation experiments, in which a certain gene is knocked out and the expression levels of other genes are observed, constitute a fundamental step in uncovering the intricate wiring diagrams in the living cell and elucidating the causal roles of genes in signaling and regulation. Here we present a novel framework for analyzing large cohorts of gene knockout experiments and their genome-wide effects on expression levels. We devise clustering-like algorithms that identify groups of genes that behave similarly with respect to the knockout data, and utilize them to predict knockout effects and to annotate physical interactions between proteins as inhibiting or activating. Differing from previous approaches, our prediction approach does not depend on physical network information; the latter is used only for the annotation task. Consequently, it is both more efficient and of wider applicability than previous methods. We evaluate our approach using a large scale collection of gene knockout experiments in yeast, comparing it to the state-of-the-art SPINE algorithm. In cross validation tests, our algorithm exhibits superior prediction accuracy, while at the same time increasing the coverage by over 25-fold. Significant coverage gains are obtained also in the annotation of the physical network. 相似文献
2.
Flowering in the short-day plant Lemna paucicostata 6746 canbe induced under continuous light by the addition of ferricyanie,ferrocyanide or KCN to M-sucrose medium. Each substance is nearly10 times more effective when the flasks are covered by glassbeakers than when cotton plugs are used. By contrast, when floweringis induced under continuous light by copper or by short-daytreatment, neither flowering nor growth are affected by whetherglass beakers or cotton plugs are used. Ferricyanide, ferrocyanideand KCN are also able to induce long-day flowering when theplants are grown on Msucrose medium in small beakers that areplaced in a covered storage dish that also contains a solutionof one of these compounds. Addition of a KOH trap to the storagedish completely blocks the flowering induced by these compounds.If [14C]ferrocyanide is added to the storage dish both the M-sucrosemedium and the plants contain significant amounts of radioactivity,the amount of radioactivity being proportional to the floweringresponse. These results indicate that ferricyanide, ferrocyanideand KCN break down to release HCN and that it is the HCN whichis responsible for inducing flowering in L. paucicostata 6746under continuous light.
1Present address: Department of Biology, Osaka Kyoiku University,Ikeda, Osaka 563, Japan.
2Present address: Institute of Horticulture, The Volcani Center,P. O. B. 6, Bet-Dagan, Israel. (Received January 17, 1983; Accepted March 24, 1983) 相似文献
3.
Hagit Shapira Meir Mouallem Menachem S. Shapiro Yosef Weisman Zvi Farfel 《Human genetics》1996,97(1):73-75
Pseudohypoparathyroidism type Ia (PHP-Ia) is a hereditary disease characterized by resistance to PTH and other hormones that act via cAMP. Patients have deficient activity of Gs, the subunit of the G protein, which couples hormone receptors to stimulation of adenylate cyclase. We describe two new mutations discovered in two sporadic patients with PHP-Ia. Using genomic DNA, we have amplified exons 2–13 of the Gs gene (GNAS1) by PCR, and sequenced the resulting products. Both patients had Albright's hereditary osteodystrophy, resistance to multiple hormones, and deficient Gs activity. In the first patient, a deletion of a C in exon 5 at codon 115 was found. In the second patient, an insertion of a C in exon 10 at codon 267 was detected. Both these heterozygous mutations cause frameshift, and predict decreased production of Gs. This report adds two new Gs mutations to the known ten mutations recently described. 相似文献
4.
Summary Lymphocyte blastogenesis was used as an assay of Immune RNA (I-RNA) activity. Normal, non-immune human lymphocytes following incubation with xenogeneic antitumor I-RNA extracted from the lymphoid organs of specifically immunized sheep underwent blastogenesis when exposed to solubilized human tumor antigens in vitro. Blastogenic responses were, unexpectedly, relatively specific for the tumor type used to immunize the I-RNA donor sheep. No significant blastogenic responses were elicited by the I-RNA extracts or by the antigen preparations themselves. This study suggests that normal, human lymphocytes incubated (sensitized) with I-RNA, in vitro, behave, in terms of antigen recognition, like lymphocytes which have previously been sensitized to tumor antigens and demonstrates that xenogeneic Immune RNA will mediate afferent limb immune responses to human tumor antigens.Supported, in part, by Public Health Service Grant CA-18321 from the National Institute of Health 相似文献
5.
Reizel Y Itzkovitz S Adar R Elbaz J Jinich A Chapal-Ilani N Maruvka YE Nevo N Marx Z Horovitz I Wasserstrom A Mayo A Shur I Benayahu D Skorecki K Segal E Dekel N Shapiro E 《PLoS genetics》2012,8(2):e1002477
Fundamental aspects of embryonic and post-natal development, including maintenance of the mammalian female germline, are largely unknown. Here we employ a retrospective, phylogenetic-based method for reconstructing cell lineage trees utilizing somatic mutations accumulated in microsatellites, to study female germline dynamics in mice. Reconstructed cell lineage trees can be used to estimate lineage relationships between different cell types, as well as cell depth (number of cell divisions since the zygote). We show that, in the reconstructed mouse cell lineage trees, oocytes form clusters that are separate from hematopoietic and mesenchymal stem cells, both in young and old mice, indicating that these populations belong to distinct lineages. Furthermore, while cumulus cells sampled from different ovarian follicles are distinctly clustered on the reconstructed trees, oocytes from the left and right ovaries are not, suggesting a mixing of their progenitor pools. We also observed an increase in oocyte depth with mouse age, which can be explained either by depth-guided selection of oocytes for ovulation or by post-natal renewal. Overall, our study sheds light on substantial novel aspects of female germline preservation and development. 相似文献
6.
Yosef I Bloushtain N Shapira M Qimron U 《Applied and environmental microbiology》2004,70(12):7156-7160
We have developed a simple method for single-step cloning of any PCR product into a plasmid. A novel selection principle has been applied, in which activation of a drug selection marker is achieved following homologous recombination. In this method a DNA fragment is amplified by PCR with standard oligonucleotides that contain flanking tails derived from the host plasmid and the complete lambdaPR or rrnA1 promoter regions. The resulting PCR product is then electroporated into an Escherichia coli strain harboring both the phage lambda Red functions and the host plasmid. Upon homologous recombination of the PCR fragment into the plasmid, expression of a drug selection marker is fully induced due to restoration of its truncated promoter, thus allowing appropriate selection. Recombinant plasmid vectors encoding beta-galactosidase and neomycin phosphotransferase were constructed by using this method in two well-known Red systems. This cloning strategy significantly reduces both the time and costs associated with cloning procedures. 相似文献
7.
8.
Jotham Suez Steffen Porwollik Amir Dagan Alex Marzel Yosef Ilan Schorr Prerak T. Desai Vered Agmon Michael McClelland Galia Rahav Ohad Gal-Mor 《PloS one》2013,8(3)
Human infection with non-typhoidal Salmonella serovars (NTS) infrequently causes invasive systemic disease and bacteremia. To understand better the nature of invasive NTS (iNTS), we studied the gene content and the pathogenicity of bacteremic strains from twelve serovars (Typhimurium, Enteritidis, Choleraesuis, Dublin, Virchow, Newport, Bredeney, Heidelberg, Montevideo, Schwarzengrund, 9,12:l,v:- and Hadar). Comparative genomic hybridization using a Salmonella enterica microarray revealed a core of 3233 genes present in all of the iNTS strains, which include the Salmonella pathogenicity islands 1–5, 9, 13, 14; five fimbrial operons (bcf, csg, stb, sth, sti); three colonization factors (misL, bapA, sinH); and the invasion gene, pagN. In the iNTS variable genome, we identified 16 novel genomic islets; various NTS virulence factors; and six typhoid-associated virulence genes (tcfA, cdtB, hlyE, taiA, STY1413, STY1360), displaying a wider distribution among NTS than was previously known. Characterization of the bacteremic strains in C3H/HeN mice showed clear differences in disease manifestation. Previously unreported characterization of serovars Schwarzengrund, 9,12:l,v:-, Bredeney and Virchow in the mouse model showed low ability to elicit systemic disease, but a profound and elongated shedding of serovars Schwarzengrund and 9,12:l,v:- (as well as Enteritidis and Heidelberg) due to chronic infection of the mouse. Phenotypic comparison in macrophages and epithelial cell lines demonstrated a remarkable intra-serovar variation, but also showed that S. Typhimurium bacteremic strains tend to present lower intracellular growth than gastroenteritis isolates. Collectively, our data demonstrated a common core of virulence genes, which might be required for invasive salmonellosis, but also an impressive degree of genetic and phenotypic heterogeneity, highlighting that bacteremia is a complex phenotype, which cannot be attributed merely to an enhanced invasion or intracellular growth of a particular strain. 相似文献
9.
Migratory Masked Shrikes (Lanius nubicus) were mist-netted during the spring and autumn migrations at Eilat, Israel. Nearly four times more shrikes were trapped during spring than in autumn. This could be explained by either the species assorting to loop migration, or a higher capture rate owing to poor body condition after crossing the Sahara in spring. In spring, no differences in phenology were observed between the sex- and age-groups. In contrast, in autumn juvenile males arrived significantly later than the rest of the population. Significant differences in wing chord length were found between the four sex and age classes (adult male, adult female, juvenile male, juvenile female) both in spring and autumn. However, significant differences in body mass were found only in autumn. In spring, in both sexes, wing length and body mass changed significantly with date of arrival. Masked Shrike in spring were lighter than in autumn. The results suggest that migration over desert is energetically costly and Eilat is a very important staging place for migratory Masked Shrikes. 相似文献
10.
Abstract Fourteen species and subspecies of ixodid ticks, representing four genera, were collected from native sheep, goats, camels and cattle in Jordan. Haemaphysalis otophila was the most common species (48.1%) with Rhipicephalus sanguineus (15.3%), Boophilus kohlsi (14.4%) and Haemaphysalis sulcatus (11.6%) representing other common species among the 9,545 specimens examined. 相似文献